Co processors for speeding up drug design algorithms
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Co-processors for speeding up drug design algorithms. Advait Jain Priyanka Jindal Pulkit Gambhir Under the guidance of: Prof. M Balakrishnan Prof. Kolin Paul. Objective. To design FPGA based hardware accelerators for speeding up the energy minimization process. Single Point Precision.

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Co processors for speeding up drug design algorithms

Co-processors for speeding up drug design algorithms

Advait Jain

Priyanka Jindal

Pulkit Gambhir

Under the guidance of:

Prof. M Balakrishnan

Prof. Kolin Paul


Objective
Objective

To design FPGA based hardware accelerators for speeding up the energy minimization process.


Single point precision
Single Point Precision

minEnergyCG()

Precision lost here

diffEnergy()

evalEnergy_for_step()

Instability introduced here

Resulting in NaN

moveStep()


Single point precision1
Single Point Precision

  • Removed the instability

    • Parabolic interpolation replaced by lnsearch() whenever points are colinear.

  • Time taken to evaluate the energy increased.

  • Increase in the number of calls to evalEnergy_for_step().



Slow float vs double of evalenergy for step calls
Slow Float Vs Double: # of evalEnergy_for_step() calls



Single point precision molecule size 2008 sd 100 cg 150
Single Point Precision (Molecule Size: 2008 SD:100 CG: 150)


Reducing the number of calls
Reducing the number of Calls

  • minEnergyCG:

    • Parabolic interpolation – which 3pts to choose.

  • Lnsearch :

    • Iteratively calculates the step size.

    • When to stop the iteration determined by 2 tolerances.

  • What we did:

    • Pts for parabolic interpolation are further apart

    • Increased the tolerances till the time to minimize the energy was same as double.

    • Then profiled to check the actual energy.



Fast float vs double evalenergy for step calls
Fast Float Vs Double: # evalEnergy_for_step() calls






Conclusion from this exercise
Conclusion from this exercise

  • Located the source of instability.

  • However converting to float increased the time required for the code to run.

  • Increasing tolerances again made the code fast.

  • The energy in case of float did not agree well with double computation.



Ongoing work
Ongoing Work

  • Familiarizing ourselves with the ADM-XRC-II board.

  • Trying to understand sample code for writing to ZBT RAMs, exchanging data with the PC.

  • Overall block diagram and connections – understood.

  • Timing – need to look at in more depth.


Tentative schedule
Tentative Schedule

  • Software Profiling August

    • No. of calls

    • Cache misses

    • Effect of parameters

  • Control Flow Analysis August - September

    • Flow Diagram

    • Data parallelism

  • Floating point precision requirement

  • Exploring H/W Options Early October

    • Platform Selection

    • S/W H/W Partitioning

  • ImplementationMid-October onwards

  • Analysis


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